title: 0uM_DNCB_A549, A_331

first: Rasim

last: Barutcu

address: 6 Davis Drive

institute: ScitoVation

description:
A_331
A549_DNCB_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line


title: amc-338-eac

status: Public on May 15 2024

type: SRA

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

library_source: transcriptomic

data_processing:
Samples were sequenced on an Illumina HiSeq4000 with single 50bp reads at 100x106 reads per sample.
Data went through quality control using FastQC.
Assembly: Reads were aligned to the human reference genome (NCBI37/hg19) using STAR v2.7.1, and annotated with Gencode v32.
Supplementary files format and content: Raw counts
Supplementary files format and content: DESeq2 vst values log2 normalized

molecule: total RNA

organism: Homo sapiens

source_name: Primary Tumor Biopsy

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA/miRNA universal kit (Qiagen, Hilden, Germany). NanoDrop (Thermo Fisher, Waltham, MA) was used to measure RNA concentration. Biopsies were sent for RNA sequencing in case tumor purity was ≥ 30% and RNA concentration was above 20 ng/µL.
Library preparation was performed using Total RNAlibrary prep RiboErase (Roche, Basel, Switzerland).

tag: tissue

value: Primary Tumor Biopsy

tag: cell type

value: tumor

tag: Sex

value: male

tag: age at_diagnosis

tag: differentiation grade


title: amc-315-eac


title: 0.0316uM_DNCB_A549, A_330

city: Durham

state: NC

country: USA

description:
A_330
A549_DNCB_0.0316uM_Rep6
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

data_processing:
Reads were mapped to the Ensembl human reference genome (hg38) using HISAT2 (version 2.05) (Zhang et al. 2021).
Alternative splicing analysis of RNA-Seq data was performed with vast-tools version 2 (Tapial et al. 2017). The INCLUSION files xontain information about the quality and raw percent spliced-in (PSI) values of each replicate. The headers of the INCLUSION files contain the cell type, the chemical, the dose, and the replicate number separated by underscores '_'. More information about this file type ccan be found at: https://github.com/vastgroup/vast-tools
Assembly: hg38
Supplementary files format and content: Read count table
Supplementary files format and content: Metadata table
Supplementary files format and content: Splicing inclusion files showing the raw percent spliced-in (PSI) values

growth_protocol: A549 cells were obtained from the American Type Culture Collection (ATCC). Proliferation media consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% FBS (Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). The plating medium consisted of Dulbecco’s Modified Essential Medium (Gibco) with 10% Heat-Inactivated FBS (HI FBS; Atlanta Biologicals) and 1% penicillin-streptomycin (Gibco). For passaging, cells were washed with sterile DPBS and enzymatically removed using 0.25% trypsin-EDTA (Gibco). In preparation for the proliferation assay, A549 cells were thawed (2.0 x 106, passage 3) and placed into a T25 flask (CytoOne; USA Scientific, Ocala, FL). After 5 days in culture, cells were passaged into a T75 flask (2.0 x 106, passage 4) using a plating medium (10% HI FBS). After 5 days, cells were plated at a density of 35,000 cells/well in black-walled, clear-bottom, tissue-culture-treated 96-well plates (Greiner Bio-One) using a plating medium (10% HI FBS). Cells were cultured for 48 h in 96-well plates prior to treatment.

extract_protocol:
Nextera XT DNA Library Preparation Kit
polyA enrichment
Illumina 150bp paired-end reads

tag: cell line

tag: treatment

value: A549 cells treated with 0.0316uM DNCB


title: 207854510042_R04C02

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
Normalized average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Human primary cell DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).

tag: modification

value: skin


title: 0.01uM_DNCB_A549, A_329

description:
A_329
A549_DNCB_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.01uM DNCB


title: HAP1 WT #4 rep1

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 Center Drive

institute: NIH, NIAID

data_processing:
MinKNOW software was used to basecall reads and generate fast5 and fastq files.
Reads were mapped to hg38 using minimap2 (PMID: 29750242) using the following parameters:- x map-ont -secondary=no -ax splice –uf .
The resulting bam files were then filtered for mapping quality and unique mapping using samtools view -F 256 -q 20, and converted to RPM-normalized bigwig files.
The filtered bam file were used along with Gencode v 33 as input to subread’s (PMID: 23558742) (version 2.0.1) feature count (parameters: -L -t exon -g gene_id) to quantify gene level expression. Differential expression was determined by DESeq2 version 1.22.2 (PMID: 25516281).
Assembly: hg38
Supplementary files format and content: Excel file contains Raw Counts, DESeq normalized counts, and DESeq differential expression results comparing the MATR3 KO to the HAP1 WT samples.

growth_protocol: HAP1 cells were cultured in IMDM medium (Quality Biological, cat# 112-035-101) supplemented with 10% (vol/vol) heat-inactivated fetal calf serum (Gibco, cat# 26170-043), 100 U/mL penicillin, 100 µg/mL streptomycin (Gibco, cat# 15140-122), at 37° C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was isolated using RNAzol (Sigma, cat#R4533-100ML) per manufacturer’s instruction. RNA was quantified with Qubit RNA HS BR Assay Kit (Thermo Fisher Scientific, cat#Q10210??) and Qubit 4 Fluorimeter according to manufacturer’s instruction. RNA integrity was verified with HS RNA Kit (15NT nt) on the 5200 Fragment Analyzer (Agilent Technologies, cat# DNF-472-500) per manufacturer’s protocol.
The ONT PCR-cDNA sequencing kit (Oxford Nanopore Technologies, cat# SQK PCS-109) was used for library preparation per manufacturer’s instructions. For each sample, 50 ng of input total RNA was used. Libraries were sequenced on the MinION Mk1C using R9.4.1 flow cells (Oxford Nanopore Technologies, cat#??)

treatment_protocol: MATR3 KO clones 1 and 5 were purchased from Horizon Discovery (cat# HZGHC007500c001, HZGHC007500c004 and HZGHC007500c005) alongside Wild Type control (cat# C631_31144, batch 36899 - Clone #4)

value: KBM-7 (CML)-derived near-haploid cell line

tag: genotype

value: Wild Type


title: amc-310-eac


title: 207854510042_R16C02

value: pancreas


title: 207854510042_R14C02


title: 0.001uM_DNCB_A549, A_327

description:
A_327
A549_DNCB_0.001uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.001uM DNCB


title: amc-307-eac


title: amc-299-eac


title: 207854510042_R10C02


title: 0.001uM_DNCB_A549, A_332

description:
A_332
A549_DNCB_0.001uM_Rep3
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0uM_DNCB_A549, A_326

description:
A_326
A549_DNCB_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0uM DNCB


title: 4.3_reg3_Ki67_Tuj1_negative-negative

type: RNA

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

hyb_protocol: In situ hybridization was conducted by incubating slides with GeoMx Human Whole Transcriptome Atlas Probe Mix (NanoString) overnight at 37°C. See Nanostring slide preparation protocol for more information: https://university.nanostring.com/geomx-dsp-manual-slide-preparation-user-manual

scan_protocol: Default settings on the Nanostring GeoMx DSP were used, see: https://university.nanostring.com/geomx-dsp-instrument-user-manual.

data_processing: Oligos were processed for library preparation according to the standard Nanostring protocol, with the exception that beads were dried for 1 min instead of 5. DNA libraries were sequenced on an Illumina NovaSeq 6000 S-Prime flow cell with a read length of 2x27bp and a 5% PhiX spike-in by volume. Output .fastq files from sequencing runs were converted to .dcc using the GeoMx NGS Pipeline with default parameters. See Nanostring protocol for more specific information: https://university.nanostring.com/geomx-dsp-ngs-readout-user-manual

source_name: olfactory neuroblastoma

label_protocol: Slides were stained with fluorescence-conjugated morphology markers for two hr at RT with the following labels: Syto 83 nuclear dye (NanoString) 250nM, CD45-532 (NovusBio cat# NBP2-34528AF532) 7.50µg/mL, TUBB3-594 (Biolegend, cat# 657408) 1:50, KI67-647 (CST cat# 12075) 1:100.

extract_protocol: 5 µm sections from high quality archival ONB tissue blocks was mounted on glass slides for profiling. Two adjacent sections were cut and positioned on separate slides to allow for side-by-side H&E comparison. Following deparaffinization, antigen retrieval was performed with Tris-EDTA buffer (pH 9.0) in a steamer for 20 min. Slides were then incubated for 15 min at 37°C in PBS buffer with 0.1 µg/mL proteinase K for RNA target exposure.

value: olfactory neuroblastoma

tag: grade

value: III

tag: Stage

value: D

tag: location

value: cervical LN

value: M

tag: age


title: 4.3_reg3_Ki67_Tuj1_negative-Tuj1


title: 4.3_reg3_Ki67_Tuj1_negative-Ki-67


title: 207854510042_R01C03


title: 0.0316uM_DNCB_A549, A_325

description:
A_325
A549_DNCB_0.0316uM_Rep5
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line


title: 207854510042_R09C03


title: amc-286-eac

value: Primary Tumor Biopsy


title: 0.01uM_DNCB_A549, A_324

description:
A_324
A549_DNCB_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: amc-287-eac

value: tumor


title: 4.3_reg2_Ki67_Tuj1-Tuj1


title: 207854510042_R07C03


title: amc-258-eac

value: not determined

value: nd


title: 0.00316uM_DNCB_A549, A_323

description:
A_323
A549_DNCB_0.00316uM_Rep5
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.00316uM DNCB


title: amc-248-esc

value: female


title: 4.3_reg2_CD45_negative-negative


title: 207854510042_R13C03

value: heart (mitral valve)


title: 0.00316uM_DNCB_A549, A_328

description:
A_328
A549_DNCB_0.00316uM_Rep6
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0.001uM_DNCB_A549, A_322

description:
A_322
A549_DNCB_0.001uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207854510042_R08C02

value: colon (small bowel)


title: amc-228-eac


title: 207854510042_R03C03

value: pancreas


title: 0uM_DNCB_A549, A_321

description:
A_321
A549_DNCB_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_DNCB_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207854510042_R05C03

value: colon (ileum)


title: 1mM_Diazinon_A549, A_320

description:
A_320
A549_Diazinon_1mM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1mM Diazinon


title: 4.3_reg1_Ki67_Tuj1_negative-Tuj1

value: olfactory neuroblastoma


title: 4.3_reg2_CD45_negative-CD45

value: III


title: 207854510042_R12C03

value: colon


title: amc-207-eac

value: male


title: 4.3_reg1_Ki67_Tuj1_negative-negative

value: D

value: cervical LN

value: M


title: amc-186-eac

value: Primary Tumor Biopsy

value: tumor


title: 207854510042_R12C02


title: 207854510042_R10C03


title: amc-180-eac


title: 100uM_Diazinon_A549, A_318

description:
A_318
A549_Diazinon_100uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 100uM Diazinon


title: 4.3_reg1_Ki67_Tuj1_negative-Ki-67


title: 207854510042_R06C03


title: 4.3_reg2_Ki67_Tuj1-Ki-67


title: 4.3_reg1_CD45_negative-negative


title: 4.3_reg1_CD45_negative-CD45


title: 10uM_Diazinon_A549, A_316

description:
A_316
A549_Diazinon_10uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 10uM Diazinon


title: amc-172-eac


title: 4.2_reg7_Ki67_negative-negative

value: IV

value: nasal cavity

value: F


title: 207854510042_R02C03


title: amc-170-eac


title: 1mM_Diazinon_A549, A_315

description:
A_315
A549_Diazinon_1mM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: amc-155-eac


title: 207854510042_R04C03


title: 207854510042_R10C01

value: motor


title: amc-150-eac


title: amc-146-eac


title: 207854510042_R14C01


title: 4.2_reg7_Ki67_negative-Ki-67


title: 100uM_Diazinon_A549, A_313

description:
A_313
A549_Diazinon_100uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 31.6uM_Diazinon_A549, A_312

description:
A_312
A549_Diazinon_31.6uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 31.6uM Diazinon


title: 31.6uM_Diazinon_A549, A_317

description:
A_317
A549_Diazinon_31.6uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 316uM_Diazinon_A549, A_314

description:
A_314
A549_Diazinon_316uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 316uM Diazinon


title: amc-138-eac

value: female


title: 4.2_reg6_CD45-CD45

value: olfactory neuroblastoma


title: 207854510042_R13C01

value: cerebellum


title: amc-120-eac


title: amc-214-eac

value: male


title: 4.2_reg5_Ki67_Tuj1_negative-Tuj1

value: D


title: 207854510042_R09C01


title: 4.2_reg5_Ki67_Tuj1_negative-negative


title: 10uM_Diazinon_A549, A_311

description:
A_311
A549_Diazinon_10uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 316uM_Diazinon_A549, A_319

description:
A_319
A549_Diazinon_316uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 207854510042_R11C01


title: 4.2_reg5_Ki67_Tuj1_negative-Ki-67


title: amc-114-eac


title: 316uM_Diazinon_A549, A_309

description:
A_309
A549_Diazinon_316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 4.2_reg5_CD45-CD45


title: 1mM_Diazinon_A549, A_310

description:
A_310
A549_Diazinon_1mM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1mM Diazinon


title: TET-LOW

city: Oklahoma City

first: Willard

last: Freeman

state: OK

address: 834 NE 13th St

department: GHD

institute: Oklahoma Medical Research Foundation

library_source: genomic

data_processing:
Following sequencing, reads were trimmed from the adaptors and trimmed accordingly to the parameters: SLIDINGWINDOW:5:25 LEADING:25 TRAILING:25 HEADCROP:3 MINLEN:30 AVGQUAL:25
Reads were aligned against Panu3.0 genes references , methylation statistic analysis was performed in CLC Genomic Workbench (QIAGEN)
For statistical analysis of different methylattion and hydroxymethylation levels,a multiple paired t-tests between HL and LL samples with Benjamini–Hochberg multiple testing correction (BHMTC) was performed
Assembly: Panu 3.0
Supplementary files format and content: txt files, raw data for each sample

organism: Papio anubis

source_name: Hippocampus

extract_protocol:
The DNA was extracted by Qiagen spin columns and 200ng was converted with with or without TET2 enzyme and then APOBEC from the NEBNext Enzymatic Methyl-seq Conversion Module (#NEBE7125L; New England Inc., Ipswich, MA).
Genomic regions of interest were amplified and amplicons were subjected to Nextera XT Library Prep Kit (#FC-131-1096; Illumina Inc. San Diego, CA) for library creation and sequencing
Targeted EM-seq

value: Hippocampus

tag: library prep_kit

value: Nextera XT Library Prep Kit

value: NEBNext Enzymatic Methyl-seq Conversion Module; TET 2 enzyme included


title: amc-111-eac

value: Primary Tumor Biopsy

value: tumor


title: 100uM_Diazinon_A549, A_308

description:
A_308
A549_Diazinon_100uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 100uM Diazinon


title: amc-100-eac


title: 31.6uM_Diazinon_A549, A_307

description:
A_307
A549_Diazinon_31.6uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 4.2_reg4_Ki67_Tuj1_negative-Tuj1

value: IV

value: nasal cavity

value: F


title: TET-8308


title: TET-HIGH


title: amc-095-eac


title: TET-5904


title: 10uM_Diazinon_A549, A_306

description:
A_306
A549_Diazinon_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 10uM Diazinon


title: amc-089-eac


title: 4.2_reg4_Ki67_Tuj1_negative-negative


title: 1mM_Diazinon_A549, A_305

description:
A_305
A549_Diazinon_1mM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: TET-3909


title: TET-3406


title: 4.2_reg2_Ki67_Tuj1_negative-Tuj1


title: amc-088-eac

value: female


title: 316uM_Diazinon_A549, A_304

description:
A_304
A549_Diazinon_316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 316uM Diazinon


title: 4.2_reg2_Ki67_Tuj1_negative-negative

value: olfactory neuroblastoma


title: amc-075-eac

value: male


title: 100uM_Diazinon_A549, A_303

description:
A_303
A549_Diazinon_100uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: TET-3304


title: 4.2_reg2_Ki67_Tuj1_negative-Ki-67

value: D


title: amc-061-eac


title: TET-2608


title: amc-044-eac

value: unknown


title: 4.2_reg1_Ki67_Tuj1_negative-negative


title: 10uM_Diazinon_A549, A_301

description:
A_301
A549_Diazinon_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: amc-031-eac


title: 4.2_reg4_Ki67_Tuj1_negative-Ki-67


title: 3.16uM_Diazinon_A549, A_300

description:
A_300
A549_Diazinon_3.16uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Diazinon


title: TET-13509

value: Hippocampus

value: Nextera XT Library Prep Kit


title: TET-2512

value: NEBNext Enzymatic Methyl-seq Conversion Module; TET 2 enzyme included


title: amc-030-eac

value: Primary Tumor Biopsy

value: tumor


title: 1uM_Diazinon_A549, A_299

description:
A_299
A549_Diazinon_1uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 1uM Diazinon


title: 4.2_reg1_Ki67_Tuj1_negative-Ki-67

value: IV

value: nasal cavity


title: TET-10310


title: amc-025-eac


title: 0.316uM_Diazinon_A549, A_298

description:
A_298
A549_Diazinon_0.316uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM Diazinon


title: 4.2_reg1_Ki67_Tuj1_negative-Tuj1

value: F


title: TET-10209


title: 4.1_reg3_Tuj1-Tuj1

value: II

value: M


title: amc-024-eac

value: male


title: 4.1_reg2_Tuj1-Tuj1

value: olfactory neuroblastoma

value: D


title: amc-023-eac


title: NOTET-LOW

value: NEBNext Enzymatic Methyl-seq Conversion Module; TET2 enzyme excluded


title: 4.1_reg1_Tuj1-Tuj1


title: 0uM_Diazinon_A549, A_296

description:
A_296
A549_Diazinon_0uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0uM Diazinon


title: 31.6uM_Diazinon_A549, A_302

description:
A_302
A549_Diazinon_31.6uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 31.6uM Diazinon


title: 4.1_reg2_stroma-CD45


title: NOTET-HIGH

value: Hippocampus

value: Nextera XT Library Prep Kit


title: 3.16uM_Diazinon_A549, A_295

description:
A_295
A549_Diazinon_3.16uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Diazinon


title: NOTET-8308


title: 1uM_Diazinon_A549, A_294

description:
A_294
A549_Diazinon_1uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line


title: amc-019-eac

value: Primary Tumor Biopsy

value: tumor


title: 4.1_reg1_Ki67-Ki-67

value: nasal cavity


title: 0.316uM_Diazinon_A549, A_293

description:
A_293
A549_Diazinon_0.316uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM Diazinon


title: amc-016-esc


title: amc-319-eac


title: 4.1_reg1_CD45-CD45


title: 3.4_normal_Tuj1-Tuj1

value: normal

value: F


title: NOTET-3406


title: NOTET-3909


title: 0.1uM_Diazinon_A549, A_297

description:
A_297
A549_Diazinon_0.1uM_Rep7
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.1uM Diazinon


title: 0.1uM_Diazinon_A549, A_292

description:
A_292
A549_Diazinon_0.1uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 0uM_Diazinon_A549, A_291

description:
A_291
A549_Diazinon_0uM_Rep5
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: NOTET-3304


title: 3.4_normal_CD45_1-negative


title: amc-313-eac

value: male

value: unknown


title: 3.16uM_Diazinon_A549, A_290

description:
A_290
A549_Diazinon_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: NOTET-2608


title: 1uM_Diazinon_A549, A_289

description:
A_289
A549_Diazinon_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Diazinon


title: 3.4_normal_CD45_2-CD45

value: olfactory neuroblastoma


title: 3.4_normal_stroma-negative


title: 3.4_normal_CD45_1-CD45


title: 3.3_reg2_Tuj1-Tuj1

value: III

value: C

value: brain


title: amc-003-eac


title: NOTET-5904

value: Hippocampus

value: Nextera XT Library Prep Kit

value: NEBNext Enzymatic Methyl-seq Conversion Module; TET2 enzyme excluded


title: amc-312-eac

value: Primary Tumor Biopsy

value: female


title: amc-311-eac

value: tumor


title: 0.316uM_Diazinon_A549, A_288

description:
A_288
A549_Diazinon_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0.316uM Diazinon


title: amc-300-eac


title: NOTET-2512


title: NOTET-10310


title: 0uM_Diazinon_A549, A_286

description:
A_286
A549_Diazinon_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0uM Diazinon


title: amc-297-eac

value: unkown


title: NOTET-10209


title: 3.3_reg2_Negative-negative

value: F


title: amc-289-eac

value: male


title: amc-314-eac


title: amc-316-eac


title: 1uM_Diazinon_A549, A_284

description:
A_284
A549_Diazinon_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Diazinon


title: 3.3_reg2_Ki67-Ki-67

value: olfactory neuroblastoma


title: 7053-GB-9

city: Ann Arbor

first: Grace

last: Bushnell

state: MI

address: 2800 Plymouth Rd NCRC B26

department: Internal Medicine

institute: University of Michigan

description: CTFRpos-1, -2, -3, bulk-1, -2, -3, CTFRneg -1,-2,-3

data_processing:
Reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure quality of data
Fastq Screen was used to screen for various types of contamination
Reads were mapped to the reference genome GRCm38 using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq
Multiqc v2.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report
Assembly: GRCm38
Supplementary files format and content: txt file is the expected counts for each gene

molecule: polyA RNA

organism: Mus musculus

source_name: breast adenocarcinoma cell line

growth_protocol: D2.0R cells were maintained in DMEM with 10% FBS and 1x glutamax

extract_protocol:
RNA was isolated using the Rneasy Qiagen kit
Libraries were prepared by the University of Michigan Advanced Genomics Core

treatment_protocol: D2.0R cells were labeled with cell trace far red and 2e6 were plated in each T150 flask with 20 mL of DMEM with 2% FBS and 1x glutamax and cultured for 1 week before CTFR+ quiescent cells and CTFR- proliferative cells were FACS sorted.

value: breast adenocarcinoma cell line

value: murine mammary gland adenocarcinoma

value: one week culture in 2% FBS prior to sorting CTFR+/-


title: amc-285-eac-b


title: 7053-GB-8


title: 0.316uM_Diazinon_A549, A_283

description:
A_283
A549_Diazinon_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 3.2_reg2_neg-negative

value: II

value: D

value: cervical LN

value: M


title: NOTET-13509

value: Hippocampus

value: Nextera XT Library Prep Kit

value: NEBNext Enzymatic Methyl-seq Conversion Module; TET2 enzyme excluded


title: 0.1uM_Diazinon_A549, A_287

description:
A_287
A549_Diazinon_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0.1uM Diazinon


title: 3.3_reg1_CD45-CD45

value: III

value: C

value: brain


title: amc-283-eac

value: Primary Tumor Biopsy

value: tumor

value: male

value: unknown


title: 3.2_reg2_Tuj1-Tuj1

value: olfactory neuroblastoma


title: 0.1uM_Diazinon_A549, A_282

description:
A_282
A549_Diazinon_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: amc-274-eac


title: 7053-GB-6

value: breast adenocarcinoma cell line

value: murine mammary gland adenocarcinoma

value: one week culture in 2% FBS prior to sorting CTFR+/-


title: 0uM_Diazinon_A549, A_281

description:
A_281
A549_Diazinon_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0uM Diazinon


title: 3.16uM_Diazinon_A549, A_285

description:
A_285
A549_Diazinon_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Diazinon_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Diazinon


title: 3.3_reg1_Tuj1-Tuj1

value: F


title: 7053-GB-7


title: 7053-GB-5


title: 3.2_reg2_Ki67-Ki-67

value: II

value: D

value: cervical LN

value: M


title: amc-273-esc


title: amc-265-eac


title: 10uM_Sulforaphane_A549, A_280

description:
A_280
A549_Sulforaphane_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 10uM Sulforaphane


title: 7053-GB-4


title: amc-264-eac

value: Primary Tumor Biopsy


title: 3.16uM_Sulforaphane_A549, A_279

description:
A_279
A549_Sulforaphane_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Sulforaphane


title: 3.2_reg1_Tuj1-Tuj1


title: amc-255-eac

value: tumor

value: female


title: 3.3_reg1_Ki67-Ki-67

value: olfactory neuroblastoma

value: III

value: C

value: brain


title: 1uM_Sulforaphane_A549, A_278

description:
A_278
A549_Sulforaphane_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Sulforaphane


title: 7053-GB-2

value: breast adenocarcinoma cell line

value: murine mammary gland adenocarcinoma

value: one week culture in 2% FBS prior to sorting CTFR+/-


title: 3.2_reg1_stroma-negative

value: II

value: D


title: 0.316uM_Sulforaphane_A549, A_277

description:
A_277
A549_Sulforaphane_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM Sulforaphane


title: 7053-GB-1


title: amc-253-eac

value: male


title: 3.1_reg2_Tuj1-Tuj1

value: nasal cavity

value: M


title: 0.1uM_Sulforaphane_A549, A_276

description:
A_276
A549_Sulforaphane_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0.1uM Sulforaphane


title: 3.2_reg1_CD45-Ki-67

value: cervical LN


title: amc-237-eac

value: Primary Tumor Biopsy

value: tumor


title: 3.1_reg2_Ki67-Ki-67

value: olfactory neuroblastoma


title: Newborn Mouse Liver rep 2

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the Celescope suite from Singleron Biotechnologies to process Fastq files and aligne them to the GRCm39 reference genome
Gene expression counts of RefSeq coding genes were produced using Celescope default settings
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Liver samples from 3 newborn mice were collected on ice at D1. Single nuclei suspension was obtained from the 3 livers by Singleron Biotechnologies and then equally pooled into a single samples to be processed for single nuclei RNA sequencing.
cDNA library preparation was performed by Singleron Biotechnologies and Illumina sequencing was performed by Macrogen.

value: Liver

value: Newborn

value: WT


title: amc-236-eac

value: female


title: Newborn Mouse Liver rep 1


title: 3.16uM_Sulforaphane_A549, A_274

description:
A_274
A549_Sulforaphane_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Sulforaphane


title: amc-231-eac


title: APRIL CAR T cells +/- IL-18 replicate 2, HTO

city: New York

first: Brandon

last: Ng

state: New York

address: 417 E 68th Street, Z1419

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.0.0). The Cell Ranger generated filtered_feature_bc_matrix.h5 files were processed using the pipeline available on the shunPykeR4 GitHub repository which implements Python and R code for streamlined analysis with Scanpy5 and other python implemented tools. Genes that were not expressed in any cell, in addition to ribosomal and hemoglobin genes, were removed prior to downstream analysis. Each cell was then normalized to a total library size of 10,000 reads and gene counts were log- transformed using the log(X+1) formula, in which log denotes the natural logarithm. Principal component analysis was applied to reduce noise prior to data clustering. To select the optimal number of principal components to retain for each dataset, the knee point (eigenvalues smaller radius of curvature) was used. Leiden clustering6 was used to identify clusters within the PCA- reduced data.
Quality of the single cells was computationally assessed based on total counts, number of genes, mitochondrial and ribosomal fraction per cell, with low total counts, low number of genes (≤1000) and high mitochondrial content (≥0.2) as negative indicators of cell quality. Cells characterized by more than one negative indicator were considered as “bad” quality cells. To remove bad quality cells and contaminants in an unbiased way, we assessed them in a cluster basis rather than individually. Leiden clusters with a “bad” quality profile and/or a high number of contaminating cells were removed. Scrublet7 was used to filter out doublets.
Assembly: mm10-2020-a
Supplementary files format and content: *.h5ad: H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format

source_name: splenocytes

extract_protocol:
Cells were then labeled with HTO barcodes and sorted for CD4+ or CD8+ T-cells with CD138+ MOPC315.BM excluded. Post-sort CD4 and CD8 T-cells were then re-pooled at a 1:1 ratio. n=2 biological replicates per group, ~30,000 cells per biological replicate were submitted for sequencing.
Single-cell RNA sequencing of FACS-sorted cell suspensions was performed on the Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1. In brief, FACS- sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 1,700–2,000 cells per μl. The viability of cells was ~70%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II). Cells were captured indroplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA was purified using Dynabeads MyOne SILANE followed by PCR amplification as per manual instruction. About 30,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10x Chromium (using HTO) following a previously published protocol3. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles) at a depth of ~575 million reads per sample.

treatment_protocol: 1.2x10^6 CAR T cells were stimulated in culture for 24 hours with 2.4x10^6 MOPC315.BM myeloma cells (1:2 T cell-to-MOPC315.BM ratio). Cells were cultured in RPMI complete media lacking IL-2.

value: splenocytes

value: T cells

value: BALB/c

value: co-culture of T cells and MOPC315.BM myeloma


title: 1uM_Sulforaphane_A549, A_273

description:
A_273
A549_Sulforaphane_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Sulforaphane


title: 3.1_reg2_CD45-CD45

value: II

value: D

value: nasal cavity

value: M


title: amc-227-eac

value: Primary Tumor Biopsy

value: male


title: 3.1_reg2_Ki67-CD45

value: olfactory neuroblastoma


title: 0.316uM_Sulforaphane_A549, A_272

description:
A_272
A549_Sulforaphane_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0.316uM Sulforaphane


title: 0.1uM_Sulforaphane_A549, A_271

description:
A_271
A549_Sulforaphane_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.1uM Sulforaphane


title: APRIL CAR T cells +/- IL-18 replicate 2, GEX


title: APRIL CAR T cells +/- IL-18 replicate 1, GEX


title: amc-223-eac

value: tumor

value: female


title: amc-220-eac


title: 3.1_reg1_Tuj1-Tuj1


title: 10uM_Sulforaphane_A549, A_270

description:
A_270
A549_Sulforaphane_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 10uM Sulforaphane


title: 3.16uM_Sulforaphane_A549, A_269

description:
A_269
A549_Sulforaphane_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Sulforaphane


title: 3.1_reg1_Ki67-Ki-67


title: amc-209-eac


title: 10uM_Sulforaphane_A549, A_275

description:
A_275
A549_Sulforaphane_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: amc-217-eac


title: 2.3_reg2_Ki67-Ki-67

value: C

value: brain


title: Mga(-/-) Mouse Rep2

city: Memphis

first: Michael

last: Walsh

address: 262 Danny Thomas

institute: St Jude Children's Research Hospital

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4, Krueger F. (2012)), in order to remove potential adapters and quality trim 3’ end of reads with cutadapt program, followed by FastQC analysis
A quality score cutoff of Q20 was used and the first 15bp of each reads were also clipped to reduce the GC bias. Next, reads were mapped to the human reference genome (hg38; GRCh38.p12) with BWA mem (0.7.17-r1188), then converted to BAM format and deduplicated with fq2bam (v3.0.0.6)
Subsequently, uniquely mapped properly paired reads were extracted with samtools (v1.2), and fragments were extracted with bedtools(v2.24.0)
Assembly: GRCh38 and GRCm38
Supplementary files format and content: BigWig format

source_name: HSC

growth_protocol: MOLM-13 cells or Lin-,cKit+ HSPCs were harvested at 50,000 cells.

extract_protocol:
Open chromatin status was assessed using the assay for transposase-accessible chromatin via sequencing (ATAC-seq) kit (Active Motif, CA) following the manufacturer’s protocols.
Library prep, included in kit, was done following the manufacturer’s protocols (Active Motif, CA).

value: HSC

tag: strain


title: 2.3_reg2_Tuj1-Tuj1

value: II


title: 3.1_reg1_CD45-CD45

value: D


title: 1uM_Sulforaphane_A549, A_268

description:
A_268
A549_Sulforaphane_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Sulforaphane


title: RPM GBC Allograft rep1

description: 10X Genomic 3' GEX

data_processing:
Demulitplexed with 10x cellranger mkfastq to create fastq files with sample index (I1, I2) and read files (R1, R2).
Reads were aligned to the custom mouse genome (refdata-cellranger-mm10) from 10X Genomics plus GFP.CDS and CellTag.UTR sequences (as described in Kong et al., Nature Protocols, 2020) and firefly Luciferase (fLuc) and Venus from our Myc and Ascl1 alleles, respectively, using cellranger mkref. Count barcodes and UMIs were then generated using cellranger count v7.0.0.
Downstream visualization and further analysis of scRNA seq data was performed in R with Seurat and/or Python with Scanpy.
Assembly: Custom mm10-2020-A plus GFP.CDS, CellTag.UTR, firefly Luciferase (fLuc), and Venus sequences as indicators of Cre-mediated recombination for the Myc allele (fLuc) or Ascl1 allele (Venus).
Supplementary files format and content: Filtered feature-barcode matrices from cellranger count.

source_name: allograft tumor

extract_protocol:
Allograft tumor  was subject to enzymatic/mechanical digestion into a single cell suspension. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq.
10X Genomics Single-Cell 3' RNA Dual Index v3

value: allograft tumor

value: Rb1 fl/fl; Trp53 fl/fl; Myc T58A (RPM)


title: 2.3_reg1_Tuj1-Tuj1

value: M


title: amc-208-eac

value: Primary Tumor Biopsy

value: male


title: APRIL CAR T cells +/- IL-18 replicate 1, HTO

value: splenocytes

value: T cells

value: BALB/c

value: co-culture of T cells and MOPC315.BM myeloma


title: 0.316uM_Sulforaphane_A549, A_267

description:
A_267
A549_Sulforaphane_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0.316uM Sulforaphane


title: amc-198-eac

value: tumor

value: female


title: Mga(+/-) Mouse Rep2

value: HSC


title: 0.1uM_Sulforaphane_A549, A_266

description:
A_266
A549_Sulforaphane_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.1uM Sulforaphane


title: Mga(+/-) Mouse Rep1


title: amc-194-eac


title: amc-183-eac


title: 10uM_Sulforaphane_A549, A_265

description:
A_265
A549_Sulforaphane_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 10uM Sulforaphane


title: 2.3_reg1_Ki67-Ki-67

value: olfactory neuroblastoma

value: II

value: C

value: brain


title: Mga(+/+) Mouse Rep2


title: 2.2_reg3_normal_Tuj1-Tuj1

value: III

value: Cribriform

value: M


title: 2.2_reg4_Ki67-Ki-67


title: Mga(+/+) Mouse Rep1


title: 1uM_Sulforaphane_A549, A_263

description:
A_263
A549_Sulforaphane_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Sulforaphane


title: amc-165-eac

value: Primary Tumor Biopsy

value: male


title: amc-154-eac


title: amc-151-eac


title: 2.2_reg3_CD45_Tuj1-CD45


title: 0.1uM_Sulforaphane_A549, A_261

description:
A_261
A549_Sulforaphane_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line


title: 2673655_SJMMAML083505_D1-HOMOb_HA-HA-AB3

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used.  Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups, fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding.  Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: BigWig format
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles

tag: chip antibody

value: anti-HA, Cell signaling 37245


title: 2.2_reg3_CD45_Tuj1-Tuj1


title: 2.2_reg2_CD45_Tuj1-Tuj1


title: Mga(-/-) Mouse Rep1


title: amc-116-eac

value: tumor


title: 0.316uM_Sulforaphane_A549, A_262

description:
A_262
A549_Sulforaphane_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM Sulforaphane


title: 2673653_SJMMAML083504_D3-HOMOa_HA-HA-AB3

value: HSC


title: amc-101-eac


title: 2673651_SJMMAML083504_D1-HOMOa_IgG-IGG-AB14

value: anti-IgG, Epicypher 13-0042k


title: 3.16uM_Sulforaphane_A549, A_264

description:
A_264
A549_Sulforaphane_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Sulforaphane


title: 0.01uM_Sulforaphane_A549, A_259

description:
A_259
A549_Sulforaphane_0.01uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.01uM Sulforaphane


title: 2673652_SJMMAML083504_D2-HOMOa_H3K4me3-H3K4me3-AB12

value: anti-H3K4me3, Epicypher 13-0041


title: 2673649_SJMMAML083503_D1-HETb_HA-HA-AB3


title: 2.2_reg1_CD45_Tuj1-Tuj1

value: olfactory neuroblastoma

value: C


title: 2.2_reg2_CD45_Tuj1-CD45

value: III


title: 2.2_reg1_CD45_Tuj1-CD45

value: Cribriform


title: amc-084-eac


title: 0.00316uM_Sulforaphane_A549, A_258

description:
A_258
A549_Sulforaphane_0.00316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.00316uM Sulforaphane


title: amc-083-eac


title: 2673647_SJMMAML083502_D3-HETa_HA-HA-AB3


title: 2.2_normal2_Tuj1-Tuj1

value: M


title: 0.001uM_Sulforaphane_A549, A_257

description:
A_257
A549_Sulforaphane_0.001uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.001uM Sulforaphane


title: 2673646_SJMMAML083502_D2-HETa_H3K4me3-H3K4me3-AB12


title: amc-072-esc

value: Primary Tumor Biopsy

value: male


title: 0uM_Sulforaphane_A549, A_256

description:
A_256
A549_Sulforaphane_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0uM Sulforaphane


title: 0.0316uM_Sulforaphane_A549, A_260

description:
A_260
A549_Sulforaphane_0.0316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM Sulforaphane


title: amc-074-eac

value: tumor


title: 2.2_normal2_stroma-negative


title: 0.0316uM_Sulforaphane_A549, A_255

description:
A_255
A549_Sulforaphane_0.0316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 2673643_SJMMAML083501_D1-WTb_HA-HA-AB3

value: HSC

value: anti-HA, Cell signaling 37245


title: 2.1_reg2_CD45_Ki67_Tuj1-Tuj1

value: II

value: A

value: nasal cavity

value: F


title: 2.2_normal1_Tuj1_1-Tuj1

value: olfactory neuroblastoma

value: III

value: C


title: 0.01uM_Sulforaphane_A549, A_254

description:
A_254
A549_Sulforaphane_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.01uM Sulforaphane


title: amc-058-eac

value: unknown


title: 0.00316uM_Sulforaphane_A549, A_253

description:
A_253
A549_Sulforaphane_0.00316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.00316uM Sulforaphane


title: amc-057-eac

value: Primary Tumor Biopsy

value: male


title: 2.1_reg2_CD45_Ki67_Tuj1-Ki-67


title: 2673640_SJMMAML083500_D2-WTa_H3K4me3-H3K4me3-AB12

value: anti-H3K4me3, Epicypher 13-0041


title: 2673639_SJMMAML083500_D1-WTa_IgG-IGG-AB14

value: anti-IgG, Epicypher 13-0042k


title: 0uM_Sulforaphane_A549, A_251

description:
A_251
A549_Sulforaphane_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0uM Sulforaphane


title: 2.1_reg2_CD45_Ki67_Tuj1-CD45


title: 2673645_SJMMAML083502_D1-HETa_IgG-IGG-AB14

value: HSC


title: 2.1_reg1_Tuj1-Tuj1

value: II


title: amc-029-eac

value: tumor


title: amc-046-eac


title: amc-060-eac


title: 0.0316uM_Sulforaphane_A549, A_250

description:
A_250
A549_Sulforaphane_0.0316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM Sulforaphane


title: 0.01uM_Sulforaphane_A549, A_249

description:
A_249
A549_Sulforaphane_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 2512331_SJMMNORM080054_C6_HOMOb_H3K27Ac_AB5

value: anti-H3K27Ac, Cell signaling 8173S


title: 2512330_SJMMNORM080054_C6_HOMOb_H3K4me3_AB12


title: 2.1_reg1_CD45-CD45

value: olfactory neuroblastoma

value: A

value: nasal cavity

value: F


title: 1.3_TUJ1_reg3-Tuj1

value: M


title: 0.001uM_Sulforaphane_A549, A_252

description:
A_252
A549_Sulforaphane_0.001uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.001uM Sulforaphane


title: 0.00316uM_Sulforaphane_A549, A_248

description:
A_248
A549_Sulforaphane_0.00316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.00316uM Sulforaphane


title: amc-055-eac

value: Primary Tumor Biopsy

value: male


title: amc-009-esc

value: female


title: 2512332_SJMMNORM080054_C6_HOMOb_H3K27me3_AB4

value: anti-H3K27me3, Cell signaling 9733S


title: 2673641_SJMMAML083500_D3-WTa_HA-HA-AB3

value: anti-HA, Cell signaling 37245


title: 1.3_TUJ1_reg1-Tuj1


title: 1.3_TUJ1_reg2-Tuj1


title: 2.1_reg1_Ki67-Ki-67


title: 2512327_SJMMNORM080054_C5_HOMOa_H3K27me3_AB4

value: HSC


title: amc-020-esc

value: unknown


title: amc-007-eac

value: tumor


title: 0uM_Sulforaphane_A549, A_246

description:
A_246
A549_Sulforaphane_0uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0uM Sulforaphane


title: KO21 +DOX

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Strasse 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

data_processing:
alignment: CLC Genomics Workbench (QIAGEN) using default settings
expression levels: CLC Genomics Workbench (QIAGEN) using default settings
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts and raw transcript counts for each sample

source_name: SW480 CRC cell line

growth_protocol: Single-cell derived subclones from polyclonal cell pools of the colorectal cancer cell line SW480 harboring the episomal pRTR-p53 vector were cultured in DMEM medium with 10% FCS (Invitrogen), penicillin/streptomycin (10 units/ml), 5% CO2.

extract_protocol:
RNAeasy kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2x105 cells were seeded in 6-well format. After 24 hours, medium was replaced with fresh medium without doxycyline(DOX) or with DOX at a final concentration of 100 ng/ml for 30 hours.

tag: genotype/variation

value: LINC01021 KO


title: 2512326_SJMMNORM080054_C5_HOMOa_H3K27Ac_AB5

value: anti-H3K27Ac, Cell signaling 8173S


title: 0.0316uM_Sulforaphane_A549, A_245

description:
A_245
A549_Sulforaphane_0.0316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM Sulforaphane


title: 2512322_SJMMNORM080054_C4_HETb_H3K27me3_AB4


title: 1.2_TUJ1_reg2-Tuj1

tag: tissue

value: olfactory neuroblastoma

value: II

value: C

value: brain

value: F


title: KO21 -DOX


title: KO12 +DOX


title: 2512321_SJMMNORM080054_C4_HETb_H3K27Ac_AB5

tag: cell type


title: 0.01uM_Sulforaphane_A549, A_244

description:
A_244
A549_Sulforaphane_0.01uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.01uM Sulforaphane


title: 0.00316uM_Sulforaphane_A549, A_243

description:
A_243
A549_Sulforaphane_0.00316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.00316uM Sulforaphane


title: 0.001uM_Sulforaphane_A549, A_247

description:
A_247
A549_Sulforaphane_0.001uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.001uM Sulforaphane


title: 2512320_SJMMNORM080054_C4_HETb_H3K4me3_AB12

value: anti-H3K4me3, Epicypher 13-0041


title: KO12 -DOX


title: 1.2_Ki67_reg1-Ki-67

tag: Sex


title: 0.001uM_Sulforaphane_A549, A_242

description:
A_242
A549_Sulforaphane_0.001uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 1.2_CD45_Neg_reg2-negative


title: 1.1_TUJ1_reg3-Tuj1


title: 2512325_SJMMNORM080054_C5_HOMOa_H3K4me3_AB12

value: HSC


title: 2512317_SJMMNORM080054_C3_HETa_H3K27me3_AB4

value: anti-H3K27me3, Cell signaling 9733S


title: 1.2_TUJ1_reg1-Tuj1


title: 0uM_Sulforaphane_A549, A_241

description:
A_241
A549_Sulforaphane_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Sulfarophane_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: KO3 +DOX


title: 100uM_Paraquat_A549, A_240

description:
A_240
A549_Paraquat_100uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 100uM Paraquat


title: 2512316_SJMMNORM080054_C3_HETa_H3K27Ac_AB5


title: 1.1_TUJ1_reg3-negative


title: KO3 -DOX


title: 2512315_SJMMNORM080054_C3_HETa_H3K4me3_AB12


title: 2512312_SJMMNORM080054_C2_WTb_H3K27me3_AB4


title: wt3 +DOX

value: LINC01021 wild-type


title: wt3 -DOX


title: 10uM_Paraquat_A549, A_238

description:
A_238
A549_Paraquat_10uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 10uM Paraquat


title: wt2 +DOX


title: 1.1_TUJ1_Neg_reg2-negative


title: 1.1_TUJ1_reg1-Tuj1


title: 31.6uM_Paraquat_A549, A_239

description:
A_239
A549_Paraquat_31.6uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 31.6uM Paraquat


title: 1.1_TUJ1_Neg_reg2-Tuj1


title: 3.16uM_Paraquat_A549, A_237

description:
A_237
A549_Paraquat_3.16uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Paraquat


title: 2512311_SJMMNORM080054_C2_WTb_H3K27Ac_AB5

value: anti-H3K27Ac, Cell signaling 8173S


title: 2512310_SJMMNORM080054_C2_WTb_H3K4me3_AB12


title: wt2 -DOX


title: 1uM_Paraquat_A549, A_236

description:
A_236
A549_Paraquat_1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Paraquat


title: 1.1_Neg_reg1-negative

value: olfactory neuroblastoma

value: II

value: C


title: wt1 +DOX


title: 2512306_SJMMNORM080054_C1_WTa_H3K27Ac_AB5


title: wt1 -DOX


title: 31.6uM_Paraquat_A549, A_234

description:
A_234
A549_Paraquat_31.6uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: 1.1_Ki67_CD45_reg3-Ki-67

value: brain

value: F


title: 2512305_SJMMNORM080054_C1_WTa_H3K4me3_AB12


title: 1.1_Ki67_reg_2-Ki-67


title: 1.1_Ki67_CD45_reg3-CD45


title: rna_mbd5_rep3

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

description:
mbd5 MO rep3
mbd5MO_differentialExpression.xlsx

data_processing:
Adapter trimming by Cutadapt
Reads mapping by STAR to the transcriptome
peak calling with pureCLIP or differential gene expression with DESeq2
Assembly: dr10
Supplementary files format and content: For [Dataset 1], excel (xlsx) files, with differential expression by DESeq2. For [Dataset 2], excel (xlsx) files, with CLIP-seq peaks identified by pureCLIP algorithm

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were treated with 0.003% 1-phenyl-2-thiourea (PTU) in E3 medium to prevent pigment formation. 3-9 months-aged wild type or mbd5 mutant lines (generated in this study) were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.

extract_protocol:
For [Dataset 1], total RNAs were extracted with standard TRIzol protocol. For [Dataset 2], 76 hpf larval zebrafish were UV crosslinked and flash-frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice-cold CLIP lysis buffer (50 mM HEPES pH 7.5, 150 mM KCl, 2 mM EDTA, 0.5% (v/v) NP-40, 0.5 mM DTT, 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail, 1 × RNaseOUT Recombinant Ribonuclease Inhibitor). Pellets were lysed by rotating at 4 °C for 15 minutes after passing through a 26 G needle (BD Biosciences). Embryo suspensions were sonicated on a bioruptor (Diagenode) with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21,000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag-antibody (Abcam) conjugated protein A beads (Invitrogen) and left overnight at 4 °C on an end-to-end rotor. Beads were washed extensively with 1 ml wash buffer (50 mM HEPES pH 7.5, 300 mM KCl, 0.05% (v/v) NP-40, 1 × Halt™ Protease and Phosphatase Inhibitor Cocktail, 1 × RNaseOUT Recombinant Ribonuclease Inhibitor) at 4 °C for 5 times. Protein-RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 (Thermo Scientific) at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS-PAGE gel and gel slices at corresponding size ranges were treated by proteinase K (Invitrogen) elution. RNA was recovered with TRIZol reagent (Invitrogen). Then T4 PNK (Thermo Scientific) end repair was performed with purified RNA before library constructions.
For [Dataset 1], RNA libraries for input samples were constructed by SMARTer Stranded Total RNA-Seq Kit v2 (TaKaRa, 634417) with ribo-minus RNA as input.  For [Dataset 2], RNA libraries were constructed with NEB small RNA kit (NEB). Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired-end mode 50 bp setting.

treatment_protocol: For [Dataset 1], morpholino oligonucleotides are applied by microinjection. For [Dataset 2], FAC (F5879, Sigma-Aldrich) was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3-6 dpf every day prior to behavior analysis. DFO (D9533, Sigma-Aldrich) was dissolved in E3 medium at 150 mM and stored at -20°C. Zebrafish were treated with 0.5 mM DFO from 3-6 dpf, replenished every day, prior to behavior analysis.

value: whole embryo

value: WT

value: mbd5 MO

tag: molecule subtype

value: RiboMinus RNA


title: 10uM_Paraquat_A549, A_233

description:
A_233
A549_Paraquat_10uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Hepatocyte, freshly isolated, 3

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

data_processing:
Sequence alignment were performed using STAR aligner.
Paired reads were then counted using ‘featureCounts’ in The Subread software
Raw counts were normalized using the edgeR package
Assembly: mm10
Supplementary files format and content: tab delimited text file include normalized CPM values for each sample

source_name: liver

growth_protocol: The HOs were maintained in the original HO growth medium with growth factors (GFs) (+GF medium). The +GF medium for  HO culture contains Advanced DMEM/F12 with B27 minus vitamin A, 10mM HEPES, GlutaMAX™, and Penicillin-Streptomycin (Thermo Fisher Scientific), 15% RSPO1 conditioned medium (home-made), 3μm CHIR99021 (MCE), 50ng/ml EGF (Biolegend), 25ng/ml HGF (Biolegend), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Biolegend), 1μM A83-01 (Sigma), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 10 mM Nicotinamide (Sigma), and 1mM N-acetylcysteine (Sigma).

extract_protocol:
Organoids were retrieved from BME using Cultrex Organoid Harvesting Solution and pelleted by centrifuge at 50g for 3 minutes. RNA was isolated from the organoid pellet using PureLinkTM RNA mini kit (Thermo fisher scientific) according to the manufacturer's instruction.
DNA was removed from RNA using RapidOut DNA Removal Kit (Thermo Fisher Scientific) according to the manufacturer's instruction. After measuring RNA quantity and quality by Agilent 2200 TapeStation, 400ng-1000ng RNA per sample reaction were used for mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using xGen™ RNA Library Prep Kit (IDT) according to the manufacturer's instruction.

treatment_protocol: The HOs were switched to the maturation medium for HO maturation. The basal medium for human and mouse HO maturation is Growth factors removed (RGF) medium, which includes William's E Medium with B27 minus vitamin A, 10mM HEPES, GlutaMAXTM and Penicillin-Streptomycin (Thermo Fischer Scientific), 50μg/ml Primocin (InvivoGen), 15% RSPO1 conditioned medium (house-made), 3μM CHIR99021 (MCE), 1μM A83-01 (MCE), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 2.5 mM Nicotinamide (Sigma), and 1.25 mM N-acetylcysteine (Sigma). Additional components were added to RGF medium for hepatic maturation of HOs. For maturation of mouse HOs, these medium incude: RGF +T3: 10nM Triiodothyronine(T3) in RGF medium; RGF +DEX: 200nM dexamethasone (DEX) in RGF medium; RGF +T3 +DEX: 10nM T3 and 200nM DEX in RGF medium. For HO dedifferentiation, the HOs were cultured in the RGF +T3 condition for 6 days, and switched to +GF condition for another 6 days. To overexpress CTNNB1ΔN90 in the HOs, AAV-TBG-CTNNB1ΔN90 was mixed with fragmented HOs in BME at a concentration of 2x10^10 GC/ml during passage.

value: liver

value: Hepatocyte organoids

value: hepatocytes

value: wild type

tag: time


title: rna_mbd5_rep2

description:
mbd5 MO rep2
mbd5MO_differentialExpression.xlsx


title: 2512304_SJMMNORM080054_C1_WTa_IGG_AB14

value: HSC

value: anti-IgG, Epicypher 13-0042k


title: Hepatocyte, freshly isolated, 2

tag: cell line


title: 2512307_SJMMNORM080054_C1_WTa_H3K27me3_AB4

value: anti-H3K27me3, Cell signaling 9733S


title: Negative control blank

type: other

molecule: other


title: Hepatocyte, freshly isolated, 1

tag: treatment


title: 1uM_Paraquat_A549, A_231

description:
A_231
A549_Paraquat_1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 1uM Paraquat


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(-/-) HSCs  #3

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079784_D1_HOM

data_processing:
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.
Supplementary files format and content: tab-delimited text file for gene counts , one gene per row and one sample per column.

extract_protocol:
RNA was extracted using a quick-RNA Microprep kit (Zymo Research, CA).
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).


title: 3.16uM_Paraquat_A549, A_232

description:
A_232
A549_Paraquat_3.16uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Paraquat


title: rna_mbd5_rep1

description:
mbd5 MO rep1
mbd5MO_differentialExpression.xlsx


title: rna_control_rep3

description:
control MO rep3
mbd5MO_differentialExpression.xlsx

value: Control MO


title: 31.6uM_Paraquat_A549, A_229

description:
A_229
A549_Paraquat_31.6uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 31.6uM Paraquat


title: rna_control_rep2

description:
control MO rep2
mbd5MO_differentialExpression.xlsx


title: Hepatocyte organoids, RGF +T3, CTNNB1 deltaN90, Day6, 2

value: RGF +T3, CTNNB1 deltaN90 overexpression, Day6


title: Hepatocyte organoids, RGF +T3, CTNNB1 deltaN90, Day6, 3


title: 100uM_Paraquat_A549, A_230

description:
A_230
A549_Paraquat_100uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 100uM Paraquat


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(-/-) HSCs  #1

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079782_D1_HOM


title: rna_control_rep1

description:
control MO rep1
mbd5MO_differentialExpression.xlsx

value: whole embryo

value: WT


title: 10uM_Paraquat_A549, A_228

description:
A_228
A549_Paraquat_10uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 10uM Paraquat


title: fac_input_rep2

description:
fac_rep2
Mbd5_CLIP_peaks.xlsx

value: 1 mM FAC from 48 to 78 hpf


title: 3.16uM_Paraquat_A549, A_227

description:
A_227
A549_Paraquat_3.16uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Hepatocyte organoids, RGF +T3, CTNNB1 deltaN90, Day6, 1

value: liver

value: Hepatocyte organoids


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(+/-) HSCs  #3

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079781_D1_HET


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(+/-) HSCs  #4

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079778_D1_HET


title: fac_input_rep1

description:
fac_rep1
Mbd5_CLIP_peaks.xlsx


title: Hepatocyte organoids, +GF, CTNNB1 deltaN90, Day6,  2

value: hepatocytes

value: wild type

value: + GF, CTNNB1 deltaN90 overexpression, Day6


title: 1uM_Paraquat_A549, A_226

description:
A_226
A549_Paraquat_1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(+/-) HSCs  #2

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079780_D1_HET

value: HSC


title: fac_clip_rep2

description:
fac_rep2
Mbd5_CLIP_peaks.xlsx


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(-/-) HSCs  #2

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079783_D1_HOM


title: 100uM_Paraquat_A549, A_225

description:
A_225
A549_Paraquat_100uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line


title: Hepatocyte organoids, +GF, CTNNB1 deltaN90, Day6,  3


title: Hepatocyte organoids, +GF, CTNNB1 deltaN90, Day6, 1


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(+/-) HSCs  #1

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079779_D1_HET


title: fac_clip_rep1

description:
fac_rep1
Mbd5_CLIP_peaks.xlsx


title: 100uM_Paraquat_A549, A_235

description:
A_235
A549_Paraquat_100uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Hepatocyte organoids, dedifferentiation, 3

value: Dedifferentiation


title: Hepatocyte organoids, dedifferentiation, 2


title: dfo_input_rep2

description:
dfo_rep2
Mbd5_CLIP_peaks.xlsx

value: 0.5 mM DFO from 48 to 78 hpf


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(+/+) HSCs  #2

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079776_D1_WT


title: dfo_input_rep1

description:
dfo_rep1
Mbd5_CLIP_peaks.xlsx


title: 3.16uM_Paraquat_A549, A_222

description:
A_222
A549_Paraquat_3.16uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 3.16uM Paraquat


title: 10uM_Paraquat_A549, A_223

description:
A_223
A549_Paraquat_10uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Hepatocyte organoids, dedifferentiation, 1


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(+/+) HSCs  #1

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079774_D1_WT


title: Hepatocyte organoids, RGF +T3 +DEX, Day 12, 3

value: RGF +T3 + DEX, Day12


title: 1uM_Paraquat_A549, A_221

description:
A_221
A549_Paraquat_1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 1uM Paraquat


title: dfo_clip_rep2

description:
dfo_rep2
Mbd5_CLIP_peaks.xlsx


title: dfo_clip_rep1

description:
dfo_rep1
Mbd5_CLIP_peaks.xlsx


title: RNA-seq of cKit+ cells from Mga(-/-) C57/B6 mice #4

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076944_D1_HOM


title: 31.6uM_Paraquat_A549, A_224

description:
A_224
A549_Paraquat_31.6uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 31.6uM Paraquat


title: 0.316uM_Paraquat_A549, A_220

description:
A_220
A549_Paraquat_0.316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM Paraquat


title: ctrl_input_rep2

description:
ctrl_rep2
Mbd5_CLIP_peaks.xlsx

value: whole embryo

value: No treatment


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(+/+) HSCs  #3

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079777_D1_WT


title: RNA-seq of cKit+ cells from Mga(-/-) C57/B6 mice #3

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076943_D1_HOM


title: 0.1uM_Paraquat_A549, A_219

description:
A_219
A549_Paraquat_0.1uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.1uM Paraquat


title: ctrl_input_rep1

description:
ctrl_rep1
Mbd5_CLIP_peaks.xlsx


title: Hepatocyte organoids, RGF +T3 +DEX, Day 12, 2

value: liver


title: 0.0316uM_Paraquat_A549, A_218

description:
A_218
A549_Paraquat_0.0316uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM Paraquat


title: Hepatocyte organoids, RGF +T3 +DEX, Day 12, 1

value: Hepatocyte organoids

value: hepatocytes


title: Hepatocyte organoids, RGF +T3, Day 12, 3

value: wild type

value: RGF +T3, Day12


title: Hepatocyte organoids, RGF +T3, Day 12, 2


title: ctrl_clip_rep2

description:
ctrl_rep2
Mbd5_CLIP_peaks.xlsx


title: 0uM_Paraquat_A549, A_216

description:
A_216
A549_Paraquat_0uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: lung adenocarcinoma cell line

value: A549 cells treated with 0uM Paraquat


title: 7053-GB-3

description: CTFRpos-1, -2, -3, bulk-1, -2, -3, CTFRneg -1,-2,-3

value: breast adenocarcinoma cell line

value: murine mammary gland adenocarcinoma

value: one week culture in 2% FBS prior to sorting CTFR+/-


title: RNA-seq of cKit+ cells from Mga(-/-) C57/B6 mice #2

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076942_D1_HOM

value: HSC


title: RNA-seq of cKit+ cells from Mga(+/-) C57/B6 mice #3

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076939_D1_HET


title: RNA-seq of cKit+ cells from Mga(+/-) C57/B6 mice #2

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076938_D1_HET


title: 0.01uM_Paraquat_A549, A_217

description:
A_217
A549_Paraquat_0.01uM_Rep4
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.01uM Paraquat


title: Hepatocyte organoids, RGF +T3, Day 12, 1


title: RNA-seq of RUNX1::RUNX1T1+ cells expressed in Mga(-/-) HSCs  #4

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML079785_D1_HOM


title: 0.1uM_Paraquat_A549, A_214

description:
A_214
A549_Paraquat_0.1uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: ctrl_clip_rep1

description:
ctrl_rep1
Mbd5_CLIP_peaks.xlsx


title: RNA-seq of cKit+ cells from Mga(+/-) C57/B6 mice #1

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076937_D1_HET


title: 0.0316uM_Paraquat_A549, A_213

description:
A_213
A549_Paraquat_0.0316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: RNA-seq of cKit+ cells from Mga(+/+) C57/B6 mice #4

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076936_D1_WT


title: RNA-seq of cKit+ cells from Mga(-/-) C57/B6 mice #1

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076941_D1_HOM


title: Hepatocyte organoids, RGF +DEX, Day 6, 3

value: RGF +DEX, Day6


title: 0.01uM_Paraquat_A549, A_212

description:
A_212
A549_Paraquat_0.01uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: RNA-seq of cKit+ cells from Mga(+/+) C57/B6 mice #3

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076935_D1_WT


title: group3,Atosiban3_1

city: xinxing

first: huijie

last: yang

address: Hongqi District, Xinxiang City

country: China

institute: Xinxiang Medical University

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: Liver cancer

growth_protocol: organoids were maintained  in humidified atmosphere with 5% CO2 at 37°C with bioGenousTM Hepatocellular Carcinoma Organoid Kit Catalog: K2105-HCC

extract_protocol:
Lysis of organoids with Trizol regent and harvesting of RNA.
RNA libraries for RNA-seq were prepared using BGISEQ-500 protocols.

treatment_protocol: First, three different of human organoid samples were constructed, and then each group of samples was treated with Vehicle and 10 μM Atosiban

value: Liver cancer

value: organoid

value: human organoids

tag: group


title: Hepatocyte organoids, RGF +DEX, Day 6, 2

value: liver

tag: genotype


title: group3,Atosiban3_3


title: 0uM_Paraquat_A549, A_211

description:
A_211
A549_Paraquat_0uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: RNA-seq of cKit+ cells from Mga(+/-) C57/B6 mice #4

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076940_D1_HET


title: group3,Atosiban3_2


title: RNA-seq of cKit+ cells from Mga(+/+) C57/B6 mice #2

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076934_D1_WT


title: 0.316uM_Paraquat_A549, A_210

description:
A_210
A549_Paraquat_0.316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.316uM Paraquat


title: Hepatocyte organoids, RGF +DEX, Day 6, 1

value: Hepatocyte organoids


title: group2,Atosiban2_3


title: RNA-seq of cKit+ cells from Mga(+/+) C57/B6 mice #1

description:
SJ_MGA_mouse_RSEM_gene_count_final.txt
SJMMAML076933_D1_WT


title: group2,Atosiban2_2


title: 0.316uM_Paraquat_A549, A_215

description:
A_215
A549_Paraquat_0.316uM_Rep3
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Hepatocyte organoids, RGF +T3 +DEX, Day 6, 3

value: hepatocytes

value: RGF +T3 + DEX, Day6


title: 0.0316uM_Paraquat_A549, A_208

description:
A_208
A549_Paraquat_0.0316uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.0316uM Paraquat


title: Hepatocyte organoids, RGF +T3 +DEX, Day 6, 2

value: wild type


title: group2,Atosiban2_1


title: Liver Heat Stress_3

city: Irvine

first: Saurabh

last: Chatterjee

state: California

address: 5270 California Avenue

department: Department of Environmental and Occupational Health

institute: University of California, Irvine

data_processing:
The quality of the sequencing was first assessed using the fastQC tool (v0.11.9) on the paired end reads. Raw reads were then illumina adapter and quality trimmed and filtered by a length of 20 bases using trimmomatic (v0.39). Trimmed reads were aligned to indexed mouse reference genome mm10 using short read aligner hisat2 (v2.2.1) and gene expression levels were quantified using featureCount from Subread (v2.0.1) for all annotated genes and samples. Differential gene expression analysis was done using R package DESeq2(v1.22.2) implementing a negative binomial model of the gene count with an FDR (false discovery rate) cut-off of 0.05. PCA plots and heatmaps were generated using DESeq2(v1.22.2).
Assembly: Trimmed reads were aligned to indexed mouse reference genome mm10 using short read aligner hisat2 (v2.2.1) and gene expression levels were quantified using featureCount from Subread (v2.0.1) for all annotated genes and samples
Supplementary files format and content: Differential Gene Expression Table obtained from analysis, comparing the log2 fold changes in Control vs Heat Stress groups. Differential gene expression analysis was done using R package DESeq2(v1.22.2) implementing a negative binomial model of the gene count with an FDR (false discovery rate) cut-off of 0.05.
Supplementary files format and content: Processed data is in microsoft excel file format converted from CSV.

molecule: cytoplasmic RNA

extract_protocol:
Samples of frozen tissue were cut and weighed to obtain  25mg. The tissue was placed into a 1.7mL microfuge tube with 500uL Trizol (Life Technologies) and kept on ice. The tissue was homogenized with a disperser (IKA) with three cycles of 20 seconds of dispersing (speed 6- liver; speed 3- brain) followed by 10 seconds of rest. The tube was kept in an ice water bath during the homogenization. After the homogenization, the tube was centrifuged for 12,000 x g for 1 minute. The supernatant was removed to a new 1.7mL microfuge tube without disturbing cell debris that may have been pelleted. The remainder of the protocol followed the instructions for the Zymo Research Direct-zol RNA miniprep kit with some minor edits. An equal volume of ethanol (90-100%) was added to the supernatant and briefly vortexed. The mixture was transferred to the Zymo Spin IICR column in a collection tube and centrifuged for 30 seconds at 12,000 x g. The flow-through was discarded and 400uL of Direct-zol RNA Wash Buffer was added to the column. The column was centrifuged for 30 seconds at 12,000 x g. A mixture of DNase digestion buffer (75uL) and DNase I (5uL) was added to the column and incubated at room temperature for 15 minutes. After the DNase I incubation, 400uL of Direct-zol RNA PreWash was added to the column, followed by centrifugation for 30 seconds at 12,000 x g. The flow-through was discarded and the PreWash step was repeated. The flow through was discarded and 700uL of Direct-zol RNA Wash Buffer was added to the column and centrifuged for 2 minutes at 12,000 x g. The spin column was removed to a fresh collection tube and centrifuged again for 1 minute at 12,000 x g. To elute the RNA, 30uL of DNase/RNase-free water was added directly to the column and incubated for 5 minutes at room temperature. The RNA was eluted by centrifugation for 1 min at 16,000 x g into a new 1.7mL lo-bind RNase-free microtube. The RNA was stored at -80oC.
Library construction is performed according to the Illumina TruSeq mRNA stranded protocol. The input quantity for total RNA will be ~ 550ng and mRNA will be enriched using oligo dT magnetic beads. The enriched mRNA is chemically fragmented for three minutes. First-strand synthesis uses random primers and reverse transcriptase to make cDNA. After second-strand synthesis, the ds cDNA is cleaned using AMPure XP beads, and the cDNA is end-repaired and then the 3’ ends are adenylated. Illumina unique dual indexed adapters are ligated on the ends and the adapter ligated fragments are enriched by nine cycles of PCR. The resulting libraries will be validated by qPCR and sized by Agilent Bioanalyzer DNA high-sensitivity chip.
The concentrations for the libraries will be normalized and multiplexed together. The multiplexed libraries will be sequenced using paired-end 100 cycles chemistry on the NovaSeq 6000. We will target 20M reads per sample.

treatment_protocol: To study the underlying pathological changes in exposure to heat stress, an aging mouse model was used. Aged C57BL6/J (24 months old) mice were exposed to heat stress at 40± 0.5°C with a relative humidity of 60% ± 5% for three hours/day for 15 days mimicking a periodic heat wave exposure.

value: Liver

value: Heat Stress

value: WT


title: Liver Heat Stress_2


title: 0.01uM_Paraquat_A549, A_207

description:
A_207
A549_Paraquat_0.01uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

data_processing:
Reads were mapped to the Ensembl human reference genome (hg38) using HISAT2 (version 2.05) (Zhang et al. 2021).
Alternative splicing analysis of RNA-Seq data was performed with vast-tools version 2 (Tapial et al. 2017). The INCLUSION files xontain information about the quality and raw percent spliced-in (PSI) values of each replicate. The headers of the INCLUSION files contain the cell type, the chemical, the dose, and the replicate number separated by underscores '_'. More information about this file type ccan be found at: https://github.com/vastgroup/vast-tools
Assembly: hg38
Supplementary files format and content: Read count table
Supplementary files format and content: Metadata table
Supplementary files format and content: Splicing inclusion files showing the raw percent spliced-in (PSI) values

extract_protocol:
Nextera XT DNA Library Preparation Kit
polyA enrichment
Illumina 150bp paired-end reads

value: lung adenocarcinoma cell line


title: group1,Atosiban1_3


title: Liver Heat Stress_1


title: Hepatocyte organoids, RGF +T3 +DEX, Day 6, 1


title: group1,Atosiban1_2


title: Hepatocyte organoids, RGF +T3, Day 6, 3

value: RGF +T3, Day6


title: Liver Control_3

value: Control


title: 0.316uM_Paraquat_A549, A_205

description:
A_205
A549_Paraquat_0.316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Hepatocyte organoids, RGF +T3, Day 6, 1


title: group3,Vehicle3_3


title: 0.1uM_Paraquat_A549, A_204

description:
A_204
A549_Paraquat_0.1uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0.1uM Paraquat


title: Hepatocyte organoids, RGF +T3, Day 6, 2


title: Liver Control_2


title: 0.0316uM_Paraquat_A549, A_203

description:
A_203
A549_Paraquat_0.0316uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: Liver Control_1


title: Brain Heat Stress_3

source_name: Brain

value: Brain


title: 0.1uM_Paraquat_A549, A_209

description:
A_209
A549_Paraquat_0.1uM_Rep2
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt


title: group3,Vehicle3_2

value: Liver cancer

value: organoid


title: 0uM_Paraquat_A549, A_202

description:
A_202
A549_Paraquat_0uM_Rep1
gene_count.txt
INCLUSION_LEVELS_Paraquat_A549_MCF7.tab.gz
metadata_sample_description.txt
metadata_sample_description_fastq_vs_sampleIDs.txt
metadata_sample_description_forinclusionlevels.txt

value: A549 cells treated with 0uM Paraquat


title: Hepatocyte organoids, RGF +T3 +DEX, Day 3, 2

value: liver

value: RGF +T3 + DEX, Day3


title: Brain Heat Stress_2


title: group2,Vehicle2_3

value: human organoids